SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools? Ling Bioinformatics 7 04-02-2015 07:17 AM
annotations intervals problem roshanbernard Bioinformatics 1 01-18-2012 06:28 PM
Tool which splits bam files into specific genomic intervals? Alex Coventry Bioinformatics 2 09-15-2011 03:23 AM
BED Tools Tutorial johnny Bioinformatics 8 09-28-2010 06:07 AM
PubMed: Hybrid selection of discrete genomic intervals on custom-designed microarrays Newsbot! Literature Watch 0 05-30-2009 06:07 AM

Reply
 
Thread Tools
Old 04-22-2009, 08:40 PM   #1
quinlana
Senior Member
 
Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Default BED Tools for genomic intervals

Hi all,
I recently completed a new suite of BED Tools for comparing, among other things, overlapping intervals of genomic features in UCSC BED format.

Much of the functionality is analogous to that available on Galaxy's website. While I find Galaxy to be sublime, I much prefer doing such analyses on the command line, especially for large datasets such as those created by next-gen platforms.

These tools allow one to answer questions such as:
Which SNPs are in genes?
How many Illumina reads align to repetitive elements?
Which Segmental duplications overlap with CNVs?
How many genes are within a 10kb window of each of my CNVs?
What is the depth of sequencing coverage in my genome of interest?
I want to merge overlapping features into a single interval.
What intervals in the genome do not contain a repeat?

They are available for 64-bit LINUX and Intel Macs at:
http://people.virginia.edu/~arq5x/bedtools.html

Contact me if you have trouble or have feature requests. As time permits, I am happy to add new tools. The ones currently available were designed mainly for my needs, so I am certain I've neglected some obviously useful ones.

Also, I plan to post the source code in the next few days, as it will be a much easier way of supporting all the various OS/Chip flavors. Plus, others can hack the code to suit their needs.

All the best,
Aaron

Last edited by quinlana; 04-23-2009 at 04:05 PM. Reason: typo; more info
quinlana is offline   Reply With Quote
Old 04-23-2009, 03:48 PM   #2
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 82
Default

Wow, thanks for making these available! I've been writing really hack versions of scripts to do a lot of this... so happy to have something more reliable!
ewilbanks is offline   Reply With Quote
Old 04-23-2009, 08:32 PM   #3
quinlana
Senior Member
 
Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Lightbulb Source code now available.

Hi all,
I posted the source code for those that were having trouble with the available binaries. Installation instructions are now on the site as well as in the README you will download. I've also included some usage examples beyond what is on the website.

http://people.virginia.edu/~arq5x/bedtools.html

Cheers.
Aaron
quinlana is offline   Reply With Quote
Old 04-27-2009, 09:36 AM   #4
quinlana
Senior Member
 
Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Default Version 1.2

Hi all,
Just a note to let you know that a new release of BEDTools is now available.

What's new?

1. closestBed. Return the feature in B that is closest to A. If multiple features in B overlap A, the one with the highest overlap is returned.
2. windowBed. Added the ability to define separate windows for upstream and downstream overlaps.
3. subtractBed. Remove the portion of A that is overlapped by features in B.
4. linksBed. Creates an HTML file of intervals in a BED file. Handy for quickly navigating to interesting regions.

Aaron

Last edited by quinlana; 04-27-2009 at 10:45 AM.
quinlana is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO